Speaking to BBC Radio 4's PM programme, Lt Kevin Sullivan, command centre chief for the North Carolina coastguard, said the crew were able to keep the ship afloat for most of the night before deciding to abandon ship in the early hours of the morning.
"Our understanding is that as [the crew] were preparing to get into the life rafts the boat suddenly capsized on them," he said. "They had to swim clear of the boat and try to get in the life rafts from there."
He said it appeared two crew members had not made it into the life rafts. The 14 who did were later picked up by coastguard helicopters and suffered only minor injures.
Here you can see a movie:
BBC News - HMS Bounty abandoned amid Hurricane Sandy
Apparently it is not the first time that they take the ship to really bad weather. This was taken in 2010: